The Manchester United goalkeeper set off for the Ivory Coast following Sunday's 2-2 draw with Tottenham in hope of being ready to feature for his nation's clash with Guinea on Monday.
Onana had delayed joining up with the rest of his Cameroon teammates so he could feature for Erik ten Hag's side.
After helping United claim a share of the spoils against Spurs, Onana made the desperate journey to the Ivory Coast which saw him travel an extra 150 miles due to adverse weather conditions.
The 27-year-old finally arrived at the Charles Konan Banny Stadium in time for kick-off but was quickly told he would not be involved in the clash.
Instead, head coach Rigobert Song opted for Fabrice Ondoa of French third tier club Nimes, with Marseille's Simon Ngapandouetnbu and Devis Epassy of Saudi club Abha named as substitute goalkeepers.
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Onana was left frustrated after being axed from the matchday squad which saw former Liverpool and Senegal forward El-Hadji Diouf intervening to calm him down.
The Manchester United star was heard shouting: "If I wasn't going to play or make the team, then why did I come here on a private jet?"
Footage has since been released showing Diouf chatting to a frustrated-looking Onana inside the stadium.
Cameroon were unable to see off ten-man Guinea in their opening match and had to come from behind to salvage a 1-1 draw.
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Mohamed Bayo fired Guinea in front after ten minutes before Frank Magri levelled for Cameroon six-minutes after the interval.
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Onana could be back in contention when Cameroon take on holders Senegal on Friday in a crunch clash between the two favourites to advance from Group C.